interfaces.meshfix

MeshFix

Link to code

Wraps the executable command meshfix.

MeshFix v1.2-alpha - by Marco Attene, Mirko Windhoff, Axel Thielscher.

See also

http://jmeshlib.sourceforge.net

Sourceforge page

http://simnibs.de/installation/meshfixandgetfem

Ubuntu installation instructions

If MeshFix is used for research purposes, please cite the following paper: M. Attene - A lightweight approach to repairing digitized polygon meshes. The Visual Computer, 2010. (c) Springer.

Accepted input formats are OFF, PLY and STL. Other formats (like .msh for gmsh) are supported only partially.

Example

>>> import nipype.interfaces.meshfix as mf
>>> fix = mf.MeshFix()
>>> fix.inputs.in_file1 = 'lh-pial.stl'
>>> fix.inputs.in_file2 = 'rh-pial.stl'
>>> fix.run()                                    # doctest: +SKIP
>>> fix.cmdline
'meshfix lh-pial.stl rh-pial.stl -o lh-pial_fixed.off'

Inputs:

[Mandatory]
in_file1: (an existing file name)
        argument: ``%s``, position: 1

[Optional]
number_of_biggest_shells: (an integer (int or long))
        Only the N biggest shells are kept
        argument: ``--shells %d``
epsilon_angle: (0.0 <= a floating point number <= 2.0)
        Epsilon angle in degrees (must be between 0 and 2)
        argument: ``-a %f``
join_overlapping_largest_components: (a boolean)
        Join 2 biggest components if they overlap, remove the rest.
        argument: ``-j``
        mutually_exclusive: join_closest_components
join_closest_components: (a boolean)
        Join the closest pair of components.
        argument: ``-jc``
        mutually_exclusive: join_closest_components
quiet_mode: (a boolean)
        Quiet mode, don't write much to stdout.
        argument: ``-q``
dont_clean: (a boolean)
        Don't Clean
        argument: ``--no-clean``
save_as_stl: (a boolean)
        Result is saved in stereolithographic format (.stl)
        argument: ``--stl``
        mutually_exclusive: save_as_vrml, save_as_freesurfer_mesh
save_as_vrml: (a boolean)
        Result is saved in VRML1.0 format (.wrl)
        argument: ``--wrl``
        mutually_exclusive: save_as_stl, save_as_freesurfer_mesh
save_as_freesurfer_mesh: (a boolean)
        Result is saved in freesurfer mesh format
        argument: ``--fsmesh``
        mutually_exclusive: save_as_vrml, save_as_stl
remove_handles: (a boolean)
        Remove handles
        argument: ``--remove-handles``
uniform_remeshing_steps: (an integer (int or long))
        Number of steps for uniform remeshing of the whole mesh
        argument: ``-u %d``
        requires: uniform_remeshing_vertices
uniform_remeshing_vertices: (an integer (int or long))
        Constrains the number of vertices.Must be used with
        uniform_remeshing_steps
        argument: ``--vertices %d``
        requires: uniform_remeshing_steps
laplacian_smoothing_steps: (an integer (int or long))
        The number of laplacian smoothing steps to apply
        argument: ``--smooth %d``
x_shift: (an integer (int or long))
        Shifts the coordinates of the vertices when saving. Output must be
        in FreeSurfer format
        argument: ``--smooth %d``
cut_outer: (an integer (int or long))
        Remove triangles of 1st that are outside of the 2nd shell.
        argument: ``--cut-outer %d``
cut_inner: (an integer (int or long))
        Remove triangles of 1st that are inside of the 2nd shell. Dilate 2nd
        by N; Fill holes and keep only 1st afterwards.
        argument: ``--cut-inner %d``
decouple_inin: (an integer (int or long))
        Treat 1st file as inner, 2nd file as outer component.Resolve
        overlaps by moving inners triangles inwards. Constrain the min
        distance between the components > d.
        argument: ``--decouple-inin %d``
decouple_outin: (an integer (int or long))
        Treat 1st file as outer, 2nd file as inner component.Resolve
        overlaps by moving outers triangles inwards. Constrain the min
        distance between the components > d.
        argument: ``--decouple-outin %d``
decouple_outout: (an integer (int or long))
        Treat 1st file as outer, 2nd file as inner component.Resolve
        overlaps by moving outers triangles outwards. Constrain the min
        distance between the components > d.
        argument: ``--decouple-outout %d``
finetuning_inwards: (a boolean)
        Used to fine-tune the minimal distance between surfaces.
        argument: ``--fineTuneIn ``, position: -3
        requires: finetuning_distance, finetuning_substeps
finetuning_outwards: (a boolean)
        Similar to finetuning_inwards, but ensures minimal distance in the
        other direction
        argument: ``--fineTuneOut ``, position: -3
        mutually_exclusive: finetuning_inwards
        requires: finetuning_distance, finetuning_substeps
finetuning_distance: (a float)
        Used to fine-tune the minimal distance between surfaces.A minimal
        distance d is ensured, and reached in n substeps. When using the
        surfaces for subsequent volume meshing by gmsh, this step prevent
        too flat tetrahedra2)
        argument: ``%f``, position: -2
        requires: finetuning_substeps
finetuning_substeps: (an integer (int or long))
        Used to fine-tune the minimal distance between surfaces.A minimal
        distance d is ensured, and reached in n substeps. When using the
        surfaces for subsequent volume meshing by gmsh, this step prevent
        too flat tetrahedra2)
        argument: ``%d``, position: -1
        requires: finetuning_distance
dilation: (an integer (int or long))
        Dilate the surface by d. d < 0 means shrinking.
        argument: ``--dilate %d``
set_intersections_to_one: (a boolean)
        If the mesh contains intersections, return value = 1.If saved in
        gmsh format, intersections will be highlighted.
        argument: ``--intersect``
in_file2: (an existing file name)
        argument: ``%s``, position: 2
output_type: ('stl' or 'msh' or 'wrl' or 'vrml' or 'fs' or 'off',
          nipype default value: off)
        The output type to save the file as.
out_filename: (a file name)
        The output filename for the fixed mesh file
        argument: ``-o %s``
args: (a unicode string)
        Additional parameters to the command
        argument: ``%s``
environ: (a dictionary with keys which are a bytes or None or a value
          of class 'str' and with values which are a bytes or None or a
          value of class 'str', nipype default value: {})
        Environment variables

Outputs:

mesh_file: (an existing file name)
        The output mesh file